From NWChem
Viewed 234 times, With a total of 2 Posts
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Just Got Here
Threads 1
Posts 3
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| 3:24:14 PM PDT - Thu, Jul 28th 2011 |
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Hi all
I have recently attempted to install nwchem using openmpi and openib on our cluster on campus. All the QA tests for the modules I have installed seem to be OK.
Small molecules run fine (<20 atoms), but now I have moved onto some slightly larger metal-organic molcules (~60 molecules) and the program appears to hang while determining the best guess for the first dft scf iteration. It takes more than an hour to complete the guess using 6-31g*, even when I am importing vectors from a previous 3-21g calculation. Once it makes a first guess the DIIS scf iterations go fairly quickly.
I am not sure if I am doing something wrong or not, but I feel that it should not hang here while using 24 processors.
Any help you could provide would be greatly appreciated!
More info below:
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Just Got Here
Threads 1
Posts 3
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| 3:26:26 PM PDT - Thu, Jul 28th 2011 |
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Build Variables:
export LARGE_FILES=TRUE
export NWCHEM_TOP=/projects/damrauer/nwchem-6.0
export NWCHEM_TARGET=LINUX64
export TCGRSH=/usr/bin/ssh
export ENABLE_COMPONENT=yes
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_intel-12.0_ib
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include
export LIBMPI="-L $MPI_LIB -lmpi -lopen-pal -lopen-rte -lmpi_f90 -lmpi_f77"
export ARMCI_NETWORK=OPENIB
export IB_HOME=/usr
export IB_INCLUDE=$IB_HOME/include/infiniband
export IB_LIB=$IB_HOME/lib64
export IB_LIB_NAME="-libumad -libverbs -lpthread"
export FOPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops -unroll-aggressive"
export COPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops"
export FC=ifort
export CC=icc
export MPI_CC=icc
Input file:
START
SCRATCH_DIR /scratch/stmp00/vallett
PERMANENT_DIR /home/vallett/nwchem_output
ECHO
MEMORY total 2000 mb
TITLE "RuBpy"
INCLUDE RuBpy.geom
set "geometry" "initial RuBpy"
charge 2
basis "all 321g basis"
* library 3-21g #except Ru
end
basis "all 631g* except Ru basis"
* library 6-31g* except Ru
Ru library 3-21g
end
set "ao basis" "all 631g* except Ru basis"
dft
mult 1
xc pbe0
iterations 600
vectors input project "all 321g basis" RuBpy.movecs output RuBpy_631g.movecs
end
task dft
Output:
everything seems ok in the geometry and basis set output, until the job actually starts to run:
Filename = /home/vallett/nwchem_output/RuBpy.movecs
Old title = "RuBpy"
Old basis size = 740
Old no. of sets = 1
Old no. of MOs = 740
Old basis name = all 321g basis
Basis name on file = all 321g basis
Time after variat. SCF: 16.7
Time prior to 1st pass: 16.7
Integral file = /scratch/stmp00/vallett/RuBpy.aoints.00
Record size in doubles = 65536 No. of integs per rec = 32766
Max. records in memory = 0 Max. records in file = 64930
No. of bits per label = 16 No. of bits per value = 64
And then it stalls here for an hour or more.
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Edited On 3:27:22 PM PDT - Thu, Jul 28th 2011 by Pvallett
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Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 2
Posts 286
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| 4:52:09 PM PDT - Tue, Aug 2nd 2011 |
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It looks like it is stalling when it tries to store integrals to disk. Try running this calculation with setting "direct" in the "scf" block.
Bert
Quote:Pvallett Jul 28th 10:26 pm== Build Variables: ==
export LARGE_FILES=TRUE
export NWCHEM_TOP=/projects/damrauer/nwchem-6.0
export NWCHEM_TARGET=LINUX64
export TCGRSH=/usr/bin/ssh
export ENABLE_COMPONENT=yes
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_intel-12.0_ib
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include
export LIBMPI="-L $MPI_LIB -lmpi -lopen-pal -lopen-rte -lmpi_f90 -lmpi_f77"
export ARMCI_NETWORK=OPENIB
export IB_HOME=/usr
export IB_INCLUDE=$IB_HOME/include/infiniband
export IB_LIB=$IB_HOME/lib64
export IB_LIB_NAME="-libumad -libverbs -lpthread"
export FOPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops -unroll-aggressive"
export COPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops"
export FC=ifort
export CC=icc
export MPI_CC=icc
Input file:
START
SCRATCH_DIR /scratch/stmp00/vallett
PERMANENT_DIR /home/vallett/nwchem_output
ECHO
MEMORY total 2000 mb
TITLE "RuBpy"
INCLUDE RuBpy.geom
set "geometry" "initial RuBpy"
charge 2
basis "all 321g basis"
* library 3-21g #except Ru
end
basis "all 631g* except Ru basis"
* library 6-31g* except Ru
Ru library 3-21g
end
set "ao basis" "all 631g* except Ru basis"
dft
mult 1
xc pbe0
iterations 600
vectors input project "all 321g basis" RuBpy.movecs output RuBpy_631g.movecs
end
task dft
Output:
everything seems ok in the geometry and basis set output, until the job actually starts to run:
Filename = /home/vallett/nwchem_output/RuBpy.movecs
Old title = "RuBpy"
Old basis size = 740
Old no. of sets = 1
Old no. of MOs = 740
Old basis name = all 321g basis
Basis name on file = all 321g basis
Time after variat. SCF: 16.7
Time prior to 1st pass: 16.7
Integral file = /scratch/stmp00/vallett/RuBpy.aoints.00
Record size in doubles = 65536 No. of integs per rec = 32766
Max. records in memory = 0 Max. records in file = 64930
No. of bits per label = 16 No. of bits per value = 64
And then it stalls here for an hour or more. |
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